I am attempting to perform ATAQ-seq on human macrophages. I have performed the protocol, though have encountered an issue at the qPCR step (after the initial 5 cycle amplification step). I find i have no amplification at all.

I was worried it was because i lost my cell pellet during the initial wash stages so i have nanodropped my samples at various steps:

1. After the initial purification following the transposition reaction
2. After the initial 5 cycle PCR amplification step
3. After final purification step

However, i have DNA at all of these steps, indicating i haven't lost my pellet and the DNA is being amplified.

For this protocol i am using the Illumina Nextera Index Kit (FC-121-1012) as the primers.
Regarding this i have two questions:
1. Are these indices compatible with qPCR?
2. For each sample should use the same index pair used in the amplification PCR in the qPCR?